The inability to conveniently version control/differentiate/combine its database caused me to drop it after a data loss (not caused by GnuCash, but HW problems), when I had only a few month old backup and a corrupted current GnuCash savefile.
I have tried beancount (like ledger but in python) since, and I'm all into plain text accounting since. Also the UI of GnuCash always felt clunky and a bit incomprehensible at places.